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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Summary
Sequence
Coding Potentia
Genome Browser
Expression
Variation
Sequence

>Osa12LNT0114400.2

TTGCAATTTACGTGATATTATGCTTCATCTTCGTGAAAAATCGAGTATTTAAATTTTACAAACCAAAGGAGAAAGGTCATTTAAATACATCTCACATGTAGTTGGATAAGTATTAGTATGTTATCTACAATTACATGATAGGATACATAAGTATTGCTCCTCAAATATGCATAAATCTTCATTAGCTACCATCCAAATACCCAAACAAGCATATGTGCAGTATAAACATGACATGCCACCCAACTTATCGATGATCTGAAAGCTTGATTACTTGGGGTTGAAGAGAATTGCTATGGCATGGTCAGAAATGGTTTGAAGGTCCAAATGAGTTCCAAAAATTCAATAATAATCAAAATGAAGAACACCATTTGGTCACCACAAAGTTATTTTTAAGCATCGATGCAATATTTACTACTATGGACAACCAAGGTCTTGAGAGATATGTCATAGGAGGATAACTACAAAGAAGTGCCATAGAAAGAATTACTGCAACACGAGAAGTGTTGATTATTCCTAGAACTTTCACAATATGTGGGTAGATAAATGTCTGGTATATAAGTATGCTAGCACCTGTAATTGCAAGAACTTGACCAACATCCTCAGACGAGAAATTTAGTCCGCCAAATTGTTTGTCACTTTCAGACCATAGAGAAAATATCTCTGTGTAAGCCATGTCATCGAAGGAGACAATGCAGAAGAGAACAATAGATGACATTAATGGCCAATTCTTAAATAAGCTCTTATCTTTAGCTGGACCAGTGTGTTGCTTGACAAACTCTTCGAAGTCAACCAAATGTGTACTCAAAGATCCAATTTTACAATCTCAGTTCTTTCTATTGAATATTTATGTAGTGTTTCCTGTGCAAGATATCCACTGATAGCTGGCCCAACAATGAGACCTATTGCCCATGATGTGCTAACCAATGACAACCCAATGGATTGATGCTCTGGTCAACAAACTTCAACGGCATAAGCCTGTAAAGCCCGGTTGCAGTATGCTAGCTAGTTATAGTATTTCAATAGTGGATAGAAAATATGAATTTAGATAATTTAATCACCGTACTCTTATTGGTCCAAGTAAGCCATTCAATGAACCTAAAAGAAATCGTGTAGTTATCGCCATCCAATAGTGTGTACTTAGTCCAAAGAGAGTATTGAATACAAATCTGATTTCACAACACAAGGTAAAGTAATCATAGGTGGATATAAAGAAGGTAATACAAATCATTACTTACTTGGTTCAATCGGAACTGAACTAAAAAGTACTTAGGCTGAAAAAATTCCAAAAATGATAACAGGCTTCCTCCCAATACGATCTGCTACCATCCCCCAAGCAGTGGAAGTTAAAGCTCTACCAAACATATATGACGCACCTACAAAACCTGCATAGAATCCAATGTCCTCTACTCTTTTTGCAACATGCAAGTCTCTTATCATGAAGTATAAGAAGGGAAATAACGATGATATTGGCAAACATGAGACGAGGATGATGATCCAGATGTGGAAGAAGCGCATGTAGGGGATGCCGGGGTTGAGCGCCTTGCTGCGCTCCACGGCGCAGGCGGGGCAGCCCTCATGGTATTGGTACGCCATCTCCAGCAATGGCGTCGCAGCGTCGCCTGCAGCCATCTCCGCTTCTTCCTCCTCTTGCTTTGCTGTTCCTGAGCTCCTGACTCCAGG

Coding Potentia
Explanation CPC Score
noncoding -1.12041
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa12LNT0114400.2 12 1635799 G A
Osa12LNT0114400.2 12 1635955 A G
Osa12LNT0114400.2 12 1636498 C T
Osa12LNT0114400.2 12 1637890 G C
Osa12LNT0114400.2 12 1639767 A C
Osa12LNT0114400.2 12 1639975 G A
Osa12LNT0114400.2 12 1642203 T C
Osa12LNT0114400.2 12 1642953 G A
Osa12LNT0114400.2 12 1643649 A C
Osa12LNT0114400.2 12 1644967 T C
Osa12LNT0114400.2 12 1645229 C T
Osa12LNT0114400.2 12 1645275 A G
Osa12LNT0114400.2 12 1645677 G T
Osa12LNT0114400.2 12 1645773 T G
Osa12LNT0114400.2 12 1642245 A G
Osa12LNT0114400.2 12 1637147 C T
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
Osa12LNT0114400.2 DTM_#DNAt_MULE_japo_Os0102 Chr12 - 1644040 1644196 156
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa12LNT0114400.2 osa-miR5808 Cleavage 5.0 21.94 1 24
Osa12LNT0114400.2 osa-miR169f.2 Cleavage 4.5 11.354 1 21
Osa12LNT0114400.2 osa-miR435 Cleavage 5.0 10.47 1 20
Osa12LNT0114400.2 osa-miR1429-5p Cleavage 4.5 16.358 1 21
Osa12LNT0114400.2 osa-miR1442 Translation 4.5 16.336 1 20
Osa12LNT0114400.2 osa-miR1858a Translation 3.0 17.105 1 21
Osa12LNT0114400.2 osa-miR1858b Translation 3.0 17.105 1 21
Osa12LNT0114400.2 osa-miR1860-5p Cleavage 5.0 16.483 1 21
Osa12LNT0114400.2 osa-miR2098-3p Cleavage 5.0 14.797 1 20
Osa12LNT0114400.2 osa-miR2868 Translation 4.5 14.628 1 20
Osa12LNT0114400.2 osa-miR5071 Translation 4.5 11.821 1 21
Osa12LNT0114400.2 osa-miR5486 Cleavage 4.5 17.776 1 21
Osa12LNT0114400.2 osa-miR5488 Translation 4.5 16.78 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa12LNT0114400.2 12 nan Physiological trait Eating quality RM20 RM101
Osa12LNT0114400.2 12 Pi-4(t) Resistance or Tolerance Blast resistance nan nan
Osa12LNT0114400.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0114400.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0114400.2 12 nan Resistance or Tolerance Other soil stress tolerance RG9 RG241
Osa12LNT0114400.2 12 gy12 Morphological trait Seed RG869 RG98
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus